Fig. 4

Differential representation of OTUs between wild Oryza species and domesticated cultivars and landraces. Differential abundance of OTUs in cultivated or wild rice rhizosphere was assessed by fitting a local regression model with a negative binomial distribution to the data and testing for differential abundance with a likelihood ratio test as implemented in the R package DESeq2 (Love et al. 2014) in conjunction with the Phyloseq package (McMurdie and Holmes 2013). Taxa are represented as dots in the graph of fold change. Positive values indicate higher representation in cultivated rice samples. Negative values indicate higher representation in wild rice samples. Samples with a p value less than 0.05 and a mean representation over all samples higher than 1 are shown